Article
Optics
Zhenyu Jiang
Summary: OpenCorr is an open source C++ library that provides full-function modules of 2D and stereo DIC, as well as digital volume correlation (DVC) for research and development of DIC technology. Its sophisticated design makes it developer-friendly, allowing users to quickly create DIC software for specific applications and develop new algorithms. The library's computation speed has been evaluated and shown to be superior. OpenCorr has gained significant interest from the academic and industrial communities, driving the advancement and spread of DIC technology.
OPTICS AND LASERS IN ENGINEERING
(2023)
Article
Biochemical Research Methods
Sylvain Prigent, Cesar Augusto Valades-Cruz, Ludovic Leconte, Jean Salamero, Charles Kervrann
Summary: Analysis of dynamic processes like vesicles transport requires particle tracking algorithms. However, the design and implementation of these algorithms often involve combining multiple software tools, leading to difficulties in reproducibility and manual operations. To address these issues, a Python library called STracking was developed to standardize particle tracking pipelines and provide a user-friendly interface for controlling trajectory quality estimation.
Article
Computer Science, Interdisciplinary Applications
Henry Martin, Ye Hong, Nina Wiedemann, Dominik Bucher, Martin Raubal
Summary: Over the past decade, scientific studies utilizing large tracking datasets have advanced our understanding of human mobility behavior. However, standardized data processing pipelines for different data collection methods are lacking, hindering reproducibility, comparability, and transferability of methods and results in quantitative human mobility analysis. This paper presents Trackintel, an open-source Python library that standardizes human mobility analysis using a compatible data model for different tracking data types. The library covers the entire life-cycle of human mobility analysis and includes processing steps, read and write interfaces, and analysis functions. A case study with four tracking datasets demonstrates the effectiveness of Trackintel in standardizing mobility data analysis and promoting transparency and comparability in novel human mobility research. The library is available open-source at https://github.com/mie-lab/trackintel.
COMPUTERS ENVIRONMENT AND URBAN SYSTEMS
(2023)
Article
Multidisciplinary Sciences
Laura Fortunato, Mark Galassi
Summary: This article explores the intersection between free and open source software (FOSS) and computational reproducibility, arguing that anyone actively involved in the research process today is a computational researcher. It provides a primer to FOSS suitable for those concerned with research quality and sustainability, using the GNU Scientific Library as a case study. The article also discusses why the common interpretation of 'open source' as 'open code' is misplaced, emphasizing the role of FOSS in research and scholarship today.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Susi Lehtola, Antti J. Karttunen
Summary: After years of waiting, computational chemistry has finally become more accessible to the masses. This article reviews the availability of free and open source software packages that offer a wide range of functionality, allowing students to perform reasonable modeling on their own devices. The use of FOSS software simplifies the installation and updating process, and also supports comprehensive teaching strategies.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Computer Science, Interdisciplinary Applications
Howard Butler, Bradley Chambers, Preston Hartzell, Craig Glennie
Summary: PDAL is an open source library for manipulating large point cloud datasets, with support for multiple languages, focusing on concepts of stages and pipelines for reading, writing, and filtering point cloud data, providing convenient access to its functionality.
COMPUTERS & GEOSCIENCES
(2021)
Article
Robotics
Gonzalo Mier, Joao Valente, Sytze de Bruin
Summary: This letter introduces Fields2Cover, an open-source library for coverage path planning (CPP) for agricultural vehicles. The library provides a framework for planning coverage paths, developing new techniques, and benchmarking state-of-the-art algorithms. It features a modular and extensible architecture and supports various vehicles and applications. The functionalities of the library are demonstrated using 8 state-of-the-art methods and 7 objective functions in simulation and field experiments.
IEEE ROBOTICS AND AUTOMATION LETTERS
(2023)
Article
Computer Science, Software Engineering
Ann Barcomb, Klaas-Jan Stol, Brian Fitzgerald, Dirk Riehle
Summary: This article introduces the practices and concerns in managing episodic volunteers in free/libre/open source software communities. It provides a systematic framework to help community managers better manage these volunteers.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2022)
Article
Optics
Yong Su, Qingchuan Zhang
Summary: This paper introduces a free and open-source software called Glare for generation and assessment of digital speckle pattern, with functions including generating speckle patterns and rendering deformed images. Glare improves computational efficiency through fast initial value estimation algorithm and integral image method.
OPTICS AND LASERS IN ENGINEERING
(2022)
Article
Biotechnology & Applied Microbiology
Pavel Sinitcyn, Hamid Hamzeiy, Favio Salinas Soto, Daniel Itzhak, Frank McCarthy, Christoph Wichmann, Martin Steger, Uli Ohmayer, Ute Distler, Stephanie Kaspar-Schoenefeld, Nikita Prianichnikov, Sule Yilmaz, Jan Daniel Rudolph, Stefan Tenzer, Yasset Perez-Riverol, Nagarjuna Nagaraj, Sean J. Humphrey, Jurgen Cox
Summary: MaxDIA is a software platform specifically designed for analyzing DIA proteomics data within the MaxQuant environment, achieving deep proteome coverage and improved protein quantification accuracy. It provides accurate FDR estimates for hypothesis-free analysis of DIA samples.
NATURE BIOTECHNOLOGY
(2021)
Article
Computer Science, Hardware & Architecture
Nguyen Van Thieu, Seyedali Mirjalili
Summary: This paper introduces a new Python library called Mealpy for implementing nature-inspired optimization algorithms. Compared to existing libraries, Mealpy has the largest collection of classical and state-of-the-art meta-heuristic algorithms, with over 160 algorithms. It is an open-source library with a simple interface and minimal dependencies. Mealpy can be used for optimizing challenge benchmark functions as well as practical problems, such as parameter optimization for machine learning models.
JOURNAL OF SYSTEMS ARCHITECTURE
(2023)
Article
Physics, Multidisciplinary
Jonas Fankhauser, Christoph Goering, Juerg Dual
Summary: This article presents the Open-Source AcoustoFluidics Theories (OSAFT) library, a Python library for solving problems related to acoustofluidics. The library provides various theoretical models for describing acoustic scattering, acoustic streaming, and the acoustic radiation force on particles. The code is designed to be extensible, with a library of fluid and solid material models to facilitate the implementation of new theories. Comparisons between different theories are made straightforward through a unified application programming interface (API).
FRONTIERS IN PHYSICS
(2022)
Article
Computer Science, Software Engineering
Leonardo Favario
Summary: This study examines the Italian strategy for free and open source software (FOSS), which is based on norms, tools, and community. The Italian approach aims to develop a public sector that can both utilize and contribute to FOSS.
Article
Information Science & Library Science
Namjoo Choi
Summary: The purpose of this paper is to revisit and update a previous study on open source software (OSS) in the library context. By analyzing articles published between March 2013 and February 2022, the study uncovers changes and developments in research trends since the previous study. The findings show a decrease in research articles since 2010, an increase in survey research, and a focus on perceptions towards OSS as a new article topic.
ELECTRONIC LIBRARY
(2023)
Article
Computer Science, Software Engineering
Yuxing Ma, Tapajit Dey, Chris Bogart, Sadika Amreen, Marat Valiev, Adam Tutko, David Kennard, Russell Zaretzki, Audris Mockus
Summary: Open source software is essential for modern society, but limited understanding exists about the periphery of the entire OSS ecosystem. By collecting a large amount of version control data and providing capabilities to analyze it, we can better understand the connections and evolution of open source software projects.
EMPIRICAL SOFTWARE ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Segundo Jose Guzman, Alois Schloegl, Michael Frotscher, Peter Jonas
Review
Engineering, Biomedical
Tilmann H. Sander, Thomas R. Knoesche, Alois Schloegl, Florian Kohl, Carsten H. Wolters, Jens Haueisen, Lutz Trahms
BIOMEDIZINISCHE TECHNIK
(2010)
Article
Biophysics
Alejandro Javier Pernia-Andrade, Sarit Pati Goswami, Yvonne Stickler, Ulrich Froebe, Alois Schloegl, Peter Jonas
BIOPHYSICAL JOURNAL
(2012)
Article
Engineering, Biomedical
Reinhold Scherer, Felix Lee, Alois Schloegl, Robert Leeb, Horst Bischof, Gert Pfurtscheller
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
(2008)
Letter
Clinical Neurology
Stefan Schaller, Peter Anderer, Georg Dorffner, Gerhard Kloesch, Ivo H. Machatschke, Alois Schloegl, Josef Zeitlhofer
MOVEMENT DISORDERS
(2012)
Article
Computer Science, Artificial Intelligence
Carmen Vidaurre, Nicole Kraemer, Benjamin Blankertz, Alois Schloegl
Article
Physics, Multidisciplinary
Guido Nolte, Andreas Ziehe, Vadim V. Nikulin, Alois Schloegl, Nicole Kraemer, Tom Brismar, Klaus-Robert Mueller
PHYSICAL REVIEW LETTERS
(2008)
Article
Psychology, Biological
Christof Koerner, Verena Braunstein, Matthias Stangl, Alois Schloegl, Christa Neuper, Anja Ischebeck
Article
Mathematical & Computational Biology
Gregor M. Hoerzer, Stefanie Liebe, Alois Schloegl, Nikos K. Logothetis, Gregor Rainer
FRONTIERS IN COMPUTATIONAL NEUROSCIENCE
(2010)
Article
Mathematical & Computational Biology
Carmen Vidaurre, Tilmann H. Sander, Alois Schloegl
COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE
(2011)
Article
Mathematical & Computational Biology
Segundo J. Guzman, Alois Schlogl, Christoph Schmidt-Hieber
FRONTIERS IN NEUROINFORMATICS
(2014)
Article
Computer Science, Interdisciplinary Applications
S. Jose Guzman, Alois Schloegl, Claudia Espinoza, Xiaomin Zhang, Benjamin A. Suter, Peter Jonas
Summary: Pattern separation is a fundamental brain computation that transforms small differences in input patterns into large differences in output patterns. External gamma-modulated inhibition and internal lateral inhibition are important mechanisms for pattern separation, while local connectivity and fast signaling play crucial roles in maximizing effectiveness. Specific properties of cells and synapses optimize higher-order computations in biological networks and have the potential to enhance deep learning capabilities in technical networks.
NATURE COMPUTATIONAL SCIENCE
(2021)
Proceedings Paper
Health Care Sciences & Services
Stefan Sauermann, Veronika David, Alois Schloegl, Reinhard Egelkraut, Matthias Frohner, Birgit Pohn, Philipp Urbauer, Alexander Mense
HEALTH INFORMATICS MEETS EHEALTH: DIGITAL INSIGHT - INFORMATION-DRIVEN HEALTH & CARE
(2017)
Proceedings Paper
Cardiac & Cardiovascular Systems
Paul Rubel, Danilo Pani, Alois Schloegl, Jocelyne Fayn, Fabio Badilini, Peter W. Macfarlane, Alpo Varri
2016 COMPUTING IN CARDIOLOGY CONFERENCE (CINC), VOL 43
(2016)
Review
Neurosciences
Michael Tangermann, Klaus-Robert Mueller, Ad Aertsen, Niels Birbaumer, Christoph Braun, Clemens Brunner, Robert Leeb, Carsten Mehring, Kai J. Miller, Gemot R. Mueller-Putz, Guido Nolte, Gert Pfurtscheller, Hubert Preissl, Gerwin Schalk, Alois Schoegl, Carmen Vidaurre, Stephan Waldert, Benjamin Blankertz
FRONTIERS IN NEUROSCIENCE
(2012)
